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Dramatic resurgence of malaria after 7 years of intensive vector control interventions in Eastern Uganda medRxiv. Infect. Dis. Pub Date : 2024-03-16 Moses R Kamya, Joaniter I Nankabirwa, Emmanuel Arinaitwe, John Rek, Maato Zedi, Catherine Maiteki-Sebuguzi, Jimmy Opigo, Sarah G Staedke, Ambrose Oruni, Martin J Donnelly, Bryan Greenhouse, Jessica Briggs, Paul J Krezanoski, Teun Bousema, Philip J Rosenthal, Peter Olwoch, Prasanna Jagannathan, Isabel Rodriguez-Barraquer, Grant Dorsey
Background: Tororo District, Uganda experienced a dramatic decrease in malaria burden from 2015-19 following 5 years of indoor residual spraying (IRS) with carbamate (Bendiocarb) and then organophosphate (Actellic) insecticides. However, a marked resurgence occurred in 2020, which coincided with a change to a clothianidin-based IRS formulations (Fludora Fusion/SumiShield). To quantify the magnitude
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Interventions for the management of post COVID-19 condition (long COVID): Protocol for a living systematic review & network meta-analysis medRxiv. Infect. Dis. Pub Date : 2024-03-16 Dena Zeraatkar, Michael Ling, Sarah Kirsh, Tanvir Jassal, Tyler Pitre, Samantha Chakraborty, Tari Turner, Lyn Turkstra, Roger S McIntyre, Ariel Izcovich, Lawrence Mbuagbaw, Thomas Agoritsas, Signe Flottorp, Paul Garner, Rachel Couban, Jason Busse
Background Up to 15% of survivors of COVID-19 infection experience long-term health effects, including fatigue, myalgia, and impaired cognitive function, termed post COVID-19 condition or long COVID. Several trials that study the benefits and harms of various interventions to manage long COVID have been published and hundreds more are planned or are ongoing. Trustworthy systematic reviews that clarify
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Common variants at 22q12.2 are associated with susceptibility to Tuberculosis medRxiv. Infect. Dis. Pub Date : 2024-03-15 Xuling Chang, Zheng Li, Vuong Khac Thai Phan, Thi Minh Ha Dang, Thuy Thuong Thuong Nguyen, Matthew Silcocks, Cynthia Bin Eng Chee, Thi Quynh Nhu Nguyen, Chew-Kiat Heng, Yik Ying Teo, Jian-Min Yuan, Woon-Puay Koh, Maxine Caws, Chiea Chuen Khor, Rajkumar Dorajoo, Sarah J Dunstan
Tuberculosis (TB) continues to be a leading cause of morbidity and mortality worldwide. Past genome-wide association studies (GWAS) have explored TB susceptibility across various ethnic groups, yet a significant portion of TB heritability remains unexplained. In this study, we conducted GWAS in the Singapore Chinese and Vietnamese, followed by a comprehensive meta-analysis incorporating independent
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Cost-effectiveness of PCV20 to Prevent Pneumococcal Disease in the Pediatric Population - A German Societal Perspective Analysis medRxiv. Infect. Dis. Pub Date : 2024-03-15 An Ta, Felicitas Kuehne, Maren Laurenz, Christof von Eiff, Sophie Warren, Johnna Perdrizet
Background: The 13-valent pneumococcal conjugate vaccine (PCV13) has been included by the German Standing Committee on Vaccinations for infants since 2009, resulting in major reductions in pneumococcal disease (PD). Higher-valent vaccines may further reduce PD burden. This cost-effectiveness analysis compared PCV20 under 3+1 schedule with PCV15 and PCV13, both under 2+1 schedule, in a German pediatric
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An Analysis of Controlled Human Infection Studies Registered on ClinicalTrials.gov medRxiv. Infect. Dis. Pub Date : 2024-03-15 Danny Toomey, Jupiter Adams-Phipps, James Wilkinson, John Pietro, Steffen Kamenicek, Daniel Kaufman, Euzebiusz Jamrozik, Joshua Osowicki, Meta Roestenberg, Ian Saldanha
OBJECTIVES: Controlled human infection studies (CHIS) involve intentional exposure of human volunteers to infectious agents. Given the small size of CHIS, aggregating data across studies is critical to the field. The objectives of the current analysis were to (1) evaluate the use of ClinicalTrials.gov for CHIS data reporting and (2) compare CHIS clinical trial participant flow and AE reporting in ClinicalTrials
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Investigating low birthweight and preterm birth as potential mediators in the relationship between prenatal infections and early child development: A linked administrative health data analysis medRxiv. Infect. Dis. Pub Date : 2024-03-15 Iain Hardie, Aja Murray, Josiah King, Hildigunnur Anna Hall, Kenneth Okelo, Emily Luedecke, Louise Marryat, Lucy Thompson, Helen Minnis, Michael Lombardo, Philip Wilson, Bonnie Auyeung
Background: Prenatal infections are associated with childhood developmental outcomes such as reduced cognitive abilities, emotional problems and other developmental vulnerabilities. However, there is currently a lack of research examining whether this arises due to potential intermediary variables like low birthweight or preterm birth, or due to some other mechanisms of maternal immune activation arising
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Metagenomic next-generation sequencing of cerebrospinal fluid for diagnosis of central nervous system infections: 7-year performance of a clinically validated test medRxiv. Infect. Dis. Pub Date : 2024-03-15 Patrick Benoit, Noah Brazer, Emily Kelly, Venice Servellita, Miriam Oseguera, Jenny Nguyen, Jack Tang, Mikael de Lorenzi-Tognon, Charles Omura, Jessica Streithorst, Melissa Hillberg, Danielle Ingebrigsten, Kelsey Zorn, Michael R Wilson, Tim Blicharz, Amy P. Wong, Brian O'Donovan, Brad Murray, Steve Miller, Charles Y Chiu
Studies have shown that metagenomic next-generation sequencing (mNGS) testing of cerebrospinal fluid (CSF) in central nervous system (CNS) infections can improve diagnostic yields and provide actionable information. We analyzed the results of all CSF mNGS tests (n=4,828) performed at the University of California, San Francisco (UCSF) clinical microbiology laboratory from June 2016 to April 2023. We
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Effect of implementing digital adherence technologies on the use of health care providers time and the human resource cost of tuberculosis treatment adherence support in Ethiopia medRxiv. Infect. Dis. Pub Date : 2024-03-15 Mahilet Belachew, Mamush Sahle, Demekech Gadissa, Tofik Abdurhman, Ahmed Bedru, Christopher Finn McQuaid, Gedion Teferra, Job Finn van Rest, Kristian Van Kalmthout, Degu Jerene, Katherine L Fielding, Amare W Tadesse, Nicola Foster
Background. The management of human resources for health is a key priority for resource constrained health systems. Digital adherence technologies (DATs) for treatment support offer an opportunity to reorganise existing healthcare worker workload. Historically, tuberculosis treatment services involved directly observed treatment with frequent patient visits to the clinic for treatment adherence support
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Sorting out assortativity: when can we assess the contributions of different population groups to epidemic transmission? medRxiv. Infect. Dis. Pub Date : 2024-03-15 Cyril Geismar, Peter J White, Anne Cori, Thibaut Jombart
Characterising the transmission dynamics between various population groups is critical for implementing effective outbreak control measures whilst minimising financial costs and societal disruption. Traditionally, mathematical models have primarily relied on assumptions of contact patterns to characterise transmission between groups. Thanks to technological and methodological advances, transmission
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Monitoring Report: Respiratory Viruses - February 2024 Data medRxiv. Infect. Dis. Pub Date : 2024-03-15 Samuel Gratzl, Brianna M Goodwin Cartwright, Patricia J Rodriguez, Charlotte Baker, Duy Do, Nicholas Stucky
Background: Few sources regularly monitor hospitalizations associated with respiratory viruses. This study provides current hospitalization trends associated with six common respiratory viruses: COVID-19, influenza, human metapneumovirus (HMPV), parainfluenza virus, respiratory syncytial virus (RSV), and rhinovirus. Objective: This study aims to supplement the surveillance data provided by the CDC
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Nipah Virus Therapeutics: A Systematic Review to Support Prioritisation for Clinical Trials medRxiv. Infect. Dis. Pub Date : 2024-03-15 Xin Hui S Chan, Ilsa L Haeusler, Bennett J K Choy, Md Zakiul Hassan, Junko Takata, Tara P Hurst, Luke M Jones, Shanghavie Loganathan, Elinor Harriss, Jake Dunning, Joel Tarning, Miles W Carroll, Peter W Horby, Piero L Olliaro
Nipah virus disease is a bat-borne zoonosis with person-to-person transmission, a case fatality rate of 38-75%, and recognised pandemic potential. The first reported outbreak occurred in Malaysia and Singapore in 1998, since followed by multiple outbreaks in Bangladesh and India. No therapeutics or vaccines have been licensed to date, and only few candidates are in development. This systematic review
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Treatment Outcomes of Doxycycline Use for Musculoskeletal Infections: A Systematic Review and Meta-Analysis medRxiv. Infect. Dis. Pub Date : 2024-03-13 Rawabi Aljadani, Carolina Gonzalez Bravo, Matida Bojang, Martha L. Carvour
Doxycycline is among the most commonly used antibiotics for the treatment and long-term suppression of musculoskeletal infections such as osteomyelitis and periprosthetic joint infection. We systematically reviewed clinical trials and cohort studies that examined outcomes of musculoskeletal infections treated with doxycycline. Eligible studies were published in Medline or Embase in English before March
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Pandemic ST131 Escherichia coli presenting the UPEC/EAEC and ExPEC/EAEC hybrid pathotypes recovered from extraintestinal infections in a clinical setting of the Brazilian Amazon region medRxiv. Infect. Dis. Pub Date : 2024-03-13 Nathalia S Bighi, Erica L Fonseca, Fernanda S Freitas, Sergio M Morgado, Ana Carolina Paulo Vicente
Escherichia coli is part of the commensal microbiota of human and animal gut. However, they may become pathogenic due to the acquisition of virulence factors that provide the ability to cause intestinal or extraintestinal infections, which makes E. coli the main cause of diarrheagenic diseases and urinary tract infections (UTIs) worldwide, respectively. Some strains, known as hybrids, may harbour a
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scRNA-Seq reveals elevated interferon responses and TNF-α signaling via NFkB in monocytes in children with uncomplicated malaria medRxiv. Infect. Dis. Pub Date : 2024-03-13 Collins Misita Morang'a, Riley S Drake, Vincent Nevan Miao, Nancy K Nyakoe, Dominic S.Y. Amuzu, Vincent Appiah, Yaw Aniweh, Yaw Bediako, Saikou Y Bah, Alex K Shalek, Gordon A Awandare, Thomas D Otto, Lucas Amenga Etego
Malaria causes significant morbidity and mortality worldwide, disproportionately impacting sub-Saharan Africa. Disease phenotypes associated with malarial infection can vary widely, from asymptomatic to life-threatening. To date, prevention efforts, particularly those related to vaccine development, have been hindered by an incomplete understanding of which factors impact host immune responses resulting
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Piloting wastewater-based surveillance of norovirus in England medRxiv. Infect. Dis. Pub Date : 2024-03-13 David I Walker, Jessica Witt, Wayne Rostant, Robert Burton, Vicki Davison, Jackie Ditchburn, Jane Heywood, James Lowther, Nick Evens, Reg Godwin, Nancy Peters, Jonathan Porter, Paulette Posen, Tyler Wickens, Matthew J. Wade
Wastewater–based epidemiology (WBE) gained widespread use as a tool for supporting clinical disease surveillance during the COVID–19 pandemic. There is now significant interest in the continued development of WBE for other pathogens of clinical significance. In this study, approximately 3,200 samples of wastewater from across England, previously collected for quantification of SARS–CoV–2, were re–analysed
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The association between prolonged SARS-CoV-2 symptoms and work outcomes medRxiv. Infect. Dis. Pub Date : 2024-03-13 Arjun Venkatesh, Huihui Yu, Caitlin Malicki, Michael Gottlieb, Joann G Elmore, Mandy J Hill, Ahamed H Idris, Juan Carlos C Montoy, Kelli N O'Laughlin, Kristin L Rising, Kari A Stephens, Erica S Spatz, Robert A Weinstein, the INSPIRE Group
While the early effects of the COVID-19 pandemic on the United States labor market are well-established, less is known about the long-term impact of SARS-CoV-2 infection and Long COVID on employment. To address this gap, we analyzed self-reported data from a prospective, national cohort study to estimate the effects of SARS-CoV-2 symptoms at three months post-infection on missed workdays and return
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PREVALENCE, INCIDENCE AND DETERMINANTS OF QUANTIFERON-POSITIVITY IN SOUTH AFRICAN SCHOOLCHILDREN medRxiv. Infect. Dis. Pub Date : 2024-03-13 Justine Stewart, Neil Walker, Karen Jennings, Carmen Delport, James Nuttall, Anna K Coussens, Robin Dyers, David A Jolliffe, Jonathan C. Y. Tang, William D Fraser, Robert J Wilkinson, Linda-Gail Bekker, Adrian R Martineau, Keren Middelkoop
Background: Tuberculosis (TB) control requires the understanding and disruption of TB transmission. We describe prevalence, incidence and risk factors associated with childhood TB infection in Cape Town. Methods: We report cross-sectional baseline and prospective incidence data from a large trial among primary school children living in high TB-burden communities. Prevalent infection was defined as
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Latent tuberculosis infection and incident cardiovascular and non-cardiovascular death medRxiv. Infect. Dis. Pub Date : 2024-03-12 Itai M Magodoro, Katalin Andrea Wilkinson, Brian Claggett, Aloice Aluoch, Mark J Siedner, Mpiko Ntsekhe, Ntobeko AB Ntusi, Moffat J. Nyirenda, Robert J Wilkinson
Active tuberculosis may heighten the risk of incident cardiovascular morbidity and premature mortality, whereas whether latent TB infection (LTBI) recapitulates these adverse outcomes is unclear. We evaluated the effect of LTBI on all-cause and cardiovascular-specific death among US adults who underwent tuberculin skin testing in 1999-2000 and were followed up to December 31st, 2019. We also examined
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Dynamics of T cell responses to COVID-19 vaccines and breakthrough infection in people living with HIV receiving antiretroviral therapy medRxiv. Infect. Dis. Pub Date : 2024-03-11 Sneha Datwani, Rebecca Kalikawe, Rachel Waterworth, Francis M Mwimanzi, Richard Liang, Yurou Sang, Hope R Lapointe, Peter K Cheung, F Harrison Omondi, Maggie C Duncan, Evan Brad, Sarah Speckmaier, Nadia Moran-Garcia, Mari L DeMarco, Malcolm Hedgcock, Cecilia T Costiniuk, Mark Hull, Marianne Harris, Marc Gabriel Romney, Julio SG Montaner, Zabrina Brumme, Mark A Brockman
Introduction: People living with HIV (PLWH) can exhibit impaired immune responses to vaccines. Accumulating evidence indicates that PLWH, particularly those receiving antiretroviral therapy, mount strong antibody responses to COVID-19 vaccination, but fewer studies have examined cellular immune responses to vaccination. We measured SARS-CoV-2 spike-specific CD4+ and CD8+ T cell responses generated
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Serum Phenylalanine, Myo-inositol, and 1,5-Anhydrohexitol biosignature differentiate neonatal sepsis cases from controls medRxiv. Infect. Dis. Pub Date : 2024-03-11 Riya Ahmed, Adyasha Sarangi, Pradeep Debata, Rajni Gaind, GP Kaushal, Renu Gur, Sushil Shrivastava, Kirti Nirmal, Ravinder Kaur, Sushma Nangia, Vivek Kumar, M Jeeva Sankar, RANJAN Kumar NANDA
Sepsis, a life-threatening multi-organ dysfunction by a dysregulated host response, is one of the leading causes of mortality in neonates. Current microbiology-based sepsis diagnosis is time-consuming, and identifying serum metabolite markers may help develop early screening tools and host-directed therapeutics. A set of 131 neonates (age 41.2% female) were classified as culture-positive or negative
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SARS-CoV-2 Genetic Variants and Patient Factors Associated with Hospitalization Risk medRxiv. Infect. Dis. Pub Date : 2024-03-10 Tonia Korves, David Stein, David Walburger, Tomasz Adamusiak, Seth Roberts
Variants of SARS-CoV-2 have been associated with different transmissibilities and disease severities. The present study examines SARS-CoV-2 genetic variants and their relationship to risk for hospitalization, using data from 12,538 patients from a large, multisite observational cohort study. The association of viral genomic variants and hospitalization is examined with clinical covariates, including
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Planning and adjusting the COVID-19 booster vaccination campaign to reduce disease burden medRxiv. Infect. Dis. Pub Date : 2024-03-10 Laura Di Domenico, Yair Goldberg, Vittoria Colizza
As public health policies shifted in 2023 from emergency response to long-term COVID-19 disease management, immunization programs started to face the challenge of formulating routine booster campaigns in a still highly uncertain seasonal behavior of the COVID-19 epidemic. Mathematical models assessing past booster campaigns and integrating knowledge on waning of immunity can help better inform current
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Factors associated with human papillomavirus, hepatitis A, hepatitis B and mpox vaccination uptake among gay, bisexual and other men who have sex with men in the UK, findings from the large community-based RiiSH-Mpox survey medRxiv. Infect. Dis. Pub Date : 2024-03-10 George Baldry, Dawn Phillips, Ruth Wilkie, Marta Checchi, Kate Folkard, Ruth Simmons, John Saunders, Sema Mandal, Catherine H Mercer, Hamish Mohammed, Dana Ogaz
Background: Gay, bisexual, and other men who have sex with men (GBMSM) face a disproportionate burden of sexually transmitted infections and are eligible for targeted vaccinations for hepatitis A (HAV), hepatitis B (HBV), human papilloma virus (HPV) and mpox. This study examines the sociodemographic characteristics, sexual behaviours, and sexual healthcare service (SHS) use associated with vaccination
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Seroclearance of HBsAg in Chronic Hepatitis B Patients After a Tolerance Breaking Immuno-Therapy: GM-CSF, followed by A Recombinant HBV Vaccine medRxiv. Infect. Dis. Pub Date : 2024-03-10 Feifei Yang, Shuang Geng, Hongyu Jia, Gan Zhao, Weidong Zhao, Jie Yu, Haoxiang Zhu, Huan Cai, Lishan Yang, Shuren Zhang, Xian Zhou, Chaofan Li, Fang Yu, Xiang Jin, Shijie Zhang, Xianzheng Wang, Yida Yang, Jimin Zhang, Bin Wang
Background: Chronic hepatitis B (CHB) remains incurable due to the immune system's tolerance towards the hepatitis B virus (HBV) surface antigen (HBsAg). This study aimed to achieve a functional cure by breaking HBV tolerance through immunotherapy. Methods: CHB patients were treated with either standard nucleotide analog (NA) therapy (Adefovir Dipivoxil, ADV) (cohort 1) or ADV combined with interferon-alpha
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RAPID POINT-OF-CARE DETECTION OF SARS-COV-2 BY ALVEO BE.WELL PLATFORM: ANALYTICAL AND CLINICAL EVALUATIONS medRxiv. Infect. Dis. Pub Date : 2024-03-09 Rixun Fang, Sha Coleman, Claudina Kwok, Helena Heisser, Teresa Wang, Lynn J Kim, Ali Coopersmith, Darren Crawford, Kim Ha, Joseph C Gaiteri, Yuh-Min (Johnson) Chiang
ABSTRACT BACKGROUND: The pandemic of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has had a profound global impact on human health and the economy. Early diagnosis and prompt effective treatment can reduce disease spread. At present, the majority of high-accuracy diagnostic tests for COVID-19 are conducted in specialized laboratories
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Harnessing digital tools for the management of large-scale larviciding operations: a pilot of the ZzappMalaria software system in Obuasi, Ghana medRxiv. Infect. Dis. Pub Date : 2024-03-09 Ignatius Williams, Kwame Desewu, Samuel Asiedu, Nicholas Ato Agyir, Dan Gluck, Arnon Houri-Yafin, Yonatan Fialkoff, Arbel Vigodny
Larval source management (LSM) has played a critical role in historical malaria elimination endeavors, yet its application in tropical settings has been hampered by operational hurdles and limited effectiveness. To address these issues, ZzappMalaria Ltd. developed a digital platform for the planning and implementation of LSM campaigns, the features and field efficacy of which are discussed in this
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Limited evidence of spill over of antimicrobial resistant Klebsiella pneumoniae from animal/environmental reservoirs to humans in India medRxiv. Infect. Dis. Pub Date : 2024-03-09 Jobin John Jacob, Aravind V, Benjamin S Beresford-Jones, Binesh Lal Y, Chaitra Shankar, Yesudoss M, Fiza Abdullah, Monisha Priya T, Sanika Kulkarni, Stephen Baker, Balaji Veeraraghavan, Kamini Walia
Background: Klebsiella pneumoniae is a common opportunistic pathogen known for having virulent and antimicrobial resistance (AMR) phenotypes. In addition to accumulating AMR and virulence genes, K. pneumoniae serves as a vehicle for broadly disseminating these elements into other species. Here, we applied genomic surveillance in a one-health framework to assess the impact of the human-animal-environment
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The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study medRxiv. Infect. Dis. Pub Date : 2024-03-08 Leon Peto, Nicola Fawcett, Musaiwale M Kamfose, Claire Scarborough, Andy Peniket, Robert Danby, Tim EA Peto, Derrick W Crook, Martin J Llewelyn, A Sarah Walker
Background: Better metrics to compare the impact of different antimicrobials on the gut microbiome would aid efforts to control antimicrobial resistance (AMR). Methods: The Antibiotic Resistance in the Microbiome - Oxford (ARMORD) study recruited inpatients, outpatients and healthy volunteers in Oxfordshire, UK, who provided stool samples for metagenomic sequencing. Data on previous antimicrobial use
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Exploring the role of temperature and other environmental factors in West Nile virus incidence and prediction in California counties from 2017-2022 medRxiv. Infect. Dis. Pub Date : 2024-03-08 Noah Parker
West Nile virus (WNV) is the most common mosquito-borne disease in the United States, resulting in hundreds of reported cases yearly in California alone. The transmission cycle occurs mostly in birds and mosquitoes, making meteorological conditions, such as temperature, especially important to transmission characteristics. Given that future increases in temperature are all but inevitable due to worldwide
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Physical and sociocultural factors influencing hand hygiene behaviour during COVID-19 pandemic: A cross-sectional study among traders in Lusaka District, Zambia medRxiv. Infect. Dis. Pub Date : 2024-03-08 Joyce Namukonda Siame, Liyali Libonda, Kanyata Kanyata
The COVID-19 epidemiology highlights the challenges for containment, mitigation, and control in low-resource settings like Zambia and suggests that the most vulnerable groups, particularly those living in low-income environments and depending on casual livelihoods, demand attention. This study aimed to determine factors that affect hand hygiene behavior during the COVID-19 Pandemic among traders at
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Characterizing SARS-CoV-2 Transmission Heterogeneity Between Urban and Rural Populations in Texas, USA, Using a Novel Spatial Transmission Count Statistic. medRxiv. Infect. Dis. Pub Date : 2024-03-08 Leke Lyu, Gabriella Elizabeth Veytsel, Guppy Stott, Spencer James Fox, Cody Aaron Dailey, Lambodhar Damodaran, Kayo Fujimoto, Jacky Kuo, Pamela Brown, Roger Sealy, Armand Brown, Magdy Alabady, Justin Bahl
Viral genomes contain records of geographic movements and cross-scale transmission dynamics. However, the impact of population heterogeneity, particularly among rural and urban areas, on viral spread and epidemic trajectory has been less explored due to limited data availability. Intensive and widespread efforts to collect and sequence SARS-CoV-2 viral samples have enabled the development of comparative
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Genetic susceptibility to acute viral bronchiolitis medRxiv. Infect. Dis. Pub Date : 2024-03-08 Anu Pasanen, Minna K Karjalainen, FinnGen, Matti Korppi, Mikko Hallman, Mika Ramet
Acute viral bronchiolitis is a major cause of infant hospitalizations worldwide. Childhood bronchiolitis is considered a risk factor for asthma, suggesting shared genetic factors and biological pathways. Genetic risk loci may provide new insights into disease pathogenesis. Here, we examined the genetic contributions to bronchiolitis susceptibility by analyzing 1,465 infants hospitalized for bronchiolitis
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Evaluation of a novel respiratory virus inactivating buffer for parallel RT-qPCR and quick antigen testing medRxiv. Infect. Dis. Pub Date : 2024-03-08 Sigrid Deprez, Sophia Steyaert, Mikhail Claeys, Ludwig Verhasselt, Jo Vandesompele
Since the COVID-19 pandemic, many hospitals implemented a dual testing procedure for SARS-CoV-2 to assess the infection risk of an admitted patient. To allow for a short turn-around time, rapid antigen (Ag) testing via lateral flow tests (LFT) is combined with nucleic acid amplification testing (NAAT), requiring two nasopharyngeal swab collections. In this study, a novel, universal pathogen inactivation
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Informing an investment case for Japanese encephalitis vaccine introduction in Bangladesh medRxiv. Infect. Dis. Pub Date : 2024-03-08 Mariana Perez Duque, Abu Mohd Naser, Kishor K Paul, Mahmudur Rahman, Mohammad Shafiul Alam, Hasan Mohammad Al-Amin, Mohammed Ziaur Rahman, Mohammad Enayet Hossain, Repon C Paul, Stephen P Luby, Simon Cauchemez, Jessica Vanhomwegen, Emily S Gurley, Henrik Salje
Background Japanese encephalitis virus (JEV) is a major threat to human health. Bangladesh is considering introducing a JEV vaccine, however, the investment case is hampered by a poor understanding of key aspects of JEV ecology, including underlying patterns of infection, the infection fatality ratio, and which host and vectors maintain transmission. Methods We conducted a seroprevalence study in individuals
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Broad-spectrum of non-serious adverse events following COVID-19 vaccination: A population-based cohort study in Seoul, South Korea medRxiv. Infect. Dis. Pub Date : 2024-03-07 Jee Hyun Suh, Hong Jin Kim, Min-Ho Kim, Myeong Geun Choi, Eun Mi Chun
Much of the current literature on the adverse effects occurring after the coronavirus disease-2019 (COVID-19) vaccination focused on serious adverse events (AEs). Consequently, the non-serious AEs have yet to be comprehensively elucidated. This study aims to investigate the incidence rate and risk of non-serious AEs including gynecological, hematological, dermatological, ophthalmological, otologic
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Predictors of mortality among COVID-19 patients at Kilimanjaro Christian Medical Centre in Northern Tanzania: A hospital-based retrospective cohort study medRxiv. Infect. Dis. Pub Date : 2024-03-07 Gilbert G. Waria, Florida J. Muro, Norman Jonas, Francis Sakita, Laura Shirima, Henry L. Mlay, Michael Ngowi, Elvis B. Meela, Innocent B. Mboya, Kajiru G. Kilonzo
Background COVID-19 disease is a global public health disaster causing a range of social, economic, and healthcare difficulties, border restrictions, high human loss, lockdown, and transportation challenges. Despite it being a global pandemic, there are few studies conducted in Tanzania to examine the predictors of mortality. This disease has caused a significant number of mortalities worldwide but
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Ongoing evolution of SARS-CoV-2 drives escape from mRNA vaccine-induced humoral immunity medRxiv. Infect. Dis. Pub Date : 2024-03-07 Alex L. Roederer, Yi Cao, Kerri St. Denis, Maegan L. Sheehan, Chia Jung Li, Evan C. Lam, David J. Gregory, Mark C. Poznansky, A. John Iafrate, David H. Canaday, Stefan Gravenstein, Wilfredo F. Garcia-Beltran, Alejandro Benjamin Balazs
Since the COVID-19 pandemic began in 2020, viral sequencing has documented 131 individual mutations in the viral spike protein across 48 named variants. To determine the ability of vaccine-mediated humoral immunity to keep pace with continued SARS-CoV-2 evolution, we assessed the neutralization potency of sera from 76 vaccine recipients collected after 2 to 6 immunizations against a comprehensive panel
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Genetic patterns, sublineages and dynamics of tuberculosis transmission in Cuba, a low burden country medRxiv. Infect. Dis. Pub Date : 2024-03-07 Ileana M Martinez-Rodriguez, Yoslany M Herrera-Avila, Roxana Goza-Valdes, Andrea Rodriguez-Bertheau, Raul Diaz-Rodriguez
Context: In Cuba, a country with a low incidence of tuberculosis (TB), there is no information on the dynamics of transmission of the disease for two decades. Aims: Determine the genetic patterns and sublineages of Mycobacterium tuberculosis complex (MTBC) isolates circulating in 2009 and their relationship with the epidemiological data of the patients. Settings and Design: A retrospective descriptive
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Learning from the COVID-19 pandemic: a systematic review of mathematical vaccine prioritization models medRxiv. Infect. Dis. Pub Date : 2024-03-07 Gilberto Gonzalez-Parra, Md Shahriar Mahmud, Claus Kadelka
As the world becomes ever more connected, the chance of pandemics increases as well. The recent COVID-19 pandemic and the concurrent global mass vaccine roll-out provides an ideal setting to learn from and refine our understanding of infectious disease models for better future preparedness. In this review, we systematically analyze and categorize mathematical models that have been developed to design
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Temporal changes in SARS-CoV-2 clearance kinetics and the optimal design of antiviral pharmacodynamic studies: an individual patient data meta-analysis of a randomised, controlled, adaptive platform study (PLATCOV) medRxiv. Infect. Dis. Pub Date : 2024-03-06 Phrutsamon Wongnak, William Henry Keith Schilling, Podjanee Jittamala, Simon Boyd, Viravarn Luvira, Tanaya Siripoon, Thundon Ngamprasertchai, Elizabeth M Batty, Shivani Singh, Jindarat Kouhathong, Watcharee Pagornrat, Patpannee Khanthagan, Borimas Hanboonkunupakarn, Kittiyod Poovorawan, Mayfong Mayxay, Kesinee Chotivanich, Mallika Imwong, Sasithon Pukrittayakamee, Elizabeth A Ashley, Arjen M Dondorp
Background Effective antiviral drugs prevent hospitalisation and death in COVID-19. Antiviral efficacy can be assessed efficiently in-vivo by measuring rates of SARS-CoV-2 clearance estimated from serial viral densities measured in nasopharyngeal or oropharyngeal swab eluates. We carried out an individual patient data meta-analysis of unblinded arms in the PLATCOV platform trial to characterise changes
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Amino acid profiling of COVID-19 patients blood serum medRxiv. Infect. Dis. Pub Date : 2024-03-06 Yana Russkikh, Natalya Sushentseva, Oleg Popov, Svetlana Apalko, Valentin S Shimansky, Anna Asinovskaya, Sergei Mosenko, Andrei Sarana, Sergey Scherbak
Main objectives of this study were to analyse metabolomic profile features of patients with COVID-19 using mass spectrometry techniques while taking into account the clinical and laboratory history, and to study the relationship between the severity of COVID-19 symptoms and the concentration of primary metabolites, primarily amino acids. We used frozen blood serum samples of 935 COVID-19 patients from
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XBB.1.5 mRNA COVID-19 Vaccination and Inpatient or Emergency Department Visits Among Adults Infected with SARS-CoV-2 JN.1 and XBB-Lineage Variants medRxiv. Infect. Dis. Pub Date : 2024-03-06 Matthew E. Levy, Vanessa Chilunda, Phillip R. Heaton, Deran McKeen, Jason D. Goldman, Richard E. Davis, Cynthia A. Schandl, William B. Glen, Lisa M. McEwen, Elizabeth T. Cirulli, Dana Wyman, Andrew Dei Rossi, Hang Dai, Magnus Isaksson, Nicole L. Washington, Tracy Basler, Kevin Tsan, Jason Nguyen, Jimmy Ramirez, Efren Sandoval, William Lee, James Lu, Shishi Luo
Within a multi-state viral genomic surveillance program, we conducted a case-control analysis comparing prior receipt of XBB.1.5-adapted mRNA vaccination between SARS-CoV-2-infected adults with inpatient/ED visits (proxy for severe illness) vs outpatient visits. Among 6,551 patients from September 2023-January 2024, 6.1% with inpatient/ED visits vs 12.0% with outpatient visits had received XBB.1.5
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Trends in fluoroquinolone prescribing in UK primary and secondary care between 2019 and 2023. medRxiv. Infect. Dis. Pub Date : 2024-03-05 Fergus W Hamilton, Elizabeth SR Darley, Alasdair P MacGowan
Introduction Fluoroquinolones are important, widely used antibiotics but have associations with a significant number of adverse outcomes. A recent (January 2024) decision by the UK drug regulator, the Medicines and Health Regulatory Authority (MHRA), restricted systemic use of these antibiotics to when only absolutely necessary with immediate effect. One stated reason for the ban was the failure of
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Modeling the Transmission Mitigation Impact of Testing for Infectious Diseases medRxiv. Infect. Dis. Pub Date : 2024-03-05 Casey Middleton, Daniel B Larremore
A fundamental question of any program focused on the testing and timely diagnosis of a communicable disease is its effectiveness in reducing transmission. Here, we introduce testing effectiveness (TE), the fraction by which testing and post-diagnosis isolation reduce transmission at the population scale, and a model that incorporates test specifications and usage, within-host pathogen dynamics, and
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Evaluation of statistical models of carriage to predict the impact of the 10-valent pneumococcal conjugate vaccine on invasive pneumococcal disease in Nigeria medRxiv. Infect. Dis. Pub Date : 2024-03-04 Aishatu L Adamu, John Ojal, Caroline Mburu, Katherine E Gallagher, Stefan Flasche, Kofo Odeyemi, Christy A.N Okoromah, Isa S Abubakar, Musa M Bello, Victor Inem, Angela Karani, Boniface Karia, Ifedayo M. O Adetifa, J. Anthony G Scott
Background: A substantial fraction of the population-level impact of Pneumococcal Conjugate Vaccines (PCVs) on Invasive Pneumococcal Disease (IPD) is mediated through indirect effects, i.e., their capacity to protect against carriage acquisition of vaccine serotypes (VTs) among vaccinees, thereby proportionately reducing transmission and indirectly averting invasive disease in the whole population
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Genome-wide association study between SARS-CoV-2 single nucleotide polymorphisms and virus copies during infections medRxiv. Infect. Dis. Pub Date : 2024-03-04 Ke Li, Chrispin Chaguza, Yi Ting Chew, Nicholas F.G. Chen, David Ferguson, Sameer Pandya, Nick Kerantzas, Wade Schulz, Yale SARS-CoV-2 Genomic Surveillance Initiative, Anne M. Hahn, Virginia E. Pitzer, Daniel M. Weinberger, Nathan D. Grubaugh
Variations in viral loads generated during SARS-CoV-2 infections can influence COVID-19 disease progression and the likelihood of onward transmission. However, the host and virus factors that may impact viral loads and infection dynamics are not fully understood. Here, we conducted virus whole genome sequencing and measured viral copies using RT-qPCR from 9,902 SARS-CoV-2 infections over a 2-year period
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Predisposing, enabling, and need factors influencing rapid uptake of the World Health Organization endorsed TB diagnostic technologies in Africa. medRxiv. Infect. Dis. Pub Date : 2024-03-04 Jean de Dieu IRAGENA, Achilles Katamba, Anandi Martin, Moses Joloba, Willy Ssengooba
Background: The implementation of rapid tuberculosis (TB) diagnostics is essential for TB control. Factors influencing their uptake in Africa are unknown. We conducted a survey to collect the status and document Predisposing, Enabling, and Need (PEN) factors influencing so that we understand the associated barriers and inform interventions to improve the uptake. Methods: We designed, piloted, and sent
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Cognitive Effects of Toxoplasma and CMV Infections: A Cross-Sectional Study of 557 Young Adults Considering Modulation by Sex and Rh Factor medRxiv. Infect. Dis. Pub Date : 2024-03-04 Jaroslav Flegr, Veronika Chvatalova, Lenka Priplatova, Petr Turecek, Petr Kodym, Sarka Kankova
One-third of humanity harbors a lifelong infection with Toxoplasma gondii. This parasite undergoes sexual reproduction in cats and asexual reproduction in any warm-blooded intermediate hosts. The cycle progresses as cats ingest these hosts, containing the parasite's tissue cysts. Such infections can alter behaviors in both animals and humans, potentially increasing predation risk by felines - usually
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The seroprevalence of SARS-CoV-2-specific antibodies in Australian children: a cross sectional study medRxiv. Infect. Dis. Pub Date : 2024-03-04 Archana Koirala, Jocelynne McRae, Philip N Britton, Marnie Downes, Shayal A Prasad, Suellen Nicholson, Noni E Winkler, Matthew O'Sullivan, Fatima Gondalwala, Cecile Castellano, Emma Carey, Alexandra Hendry, Nigel Crawford, Ushma Dilesh Wadia, Peter Richmond, Helen S Marshall, Julia E Clark, Joshua R Francis, Jeremy Carr, Adam Bartlett, Brendan McMullan, Justin Skowno, Donald Hannah, Andrew Davidson
Background: Following reduction of public health and social measures concurrent with SARS-CoV-2 Omicron emergence in late 2021 in Australia, COVID-19 case notification rates rose rapidly. As rates of direct viral testing and reporting dropped, true infection rates were most likely to be underestimated. Objective: To better understand infection rates and immunity in this population, we aimed to estimate
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Prevalence and risk factors associated with malaria infections at a micro-geographic level in three villages of Muheza district, north-eastern Tanzania medRxiv. Infect. Dis. Pub Date : 2024-03-04 Daniel P Challe, Filbert Francis, Misago D Seth, Juma B Tupa, Rashid A Madebe, Celine I Mandara, Emmanuel S Kigadye, Vedastus W Makene, Deus S Ishengoma
Background Despite a recent reduction in malaria morbidity and mortality, the disease remains a major cause of morbidity and mortality in Tanzania. However, the malaria burden is heterogeneous with a higher burden in some regions compared to others, suggesting that stratification of malaria burden and risk/predictors of infections is critical to guide the proper use of the current and future interventions
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Nasopharyngeal metatranscriptomics reveals host-pathogen signatures of pediatric sinusitis medRxiv. Infect. Dis. Pub Date : 2024-03-04 Nooran Abumazen, Vivian Chu, Manjot Hunjan, Briallen Lobb, Sojin Lee, Marcia Kurs-Lasky, John V Williams, William MacDonald, Monika Johnson, Jeremy A Hirota, Nader Shaikh, Andrew C Doxey
Acute sinusitis (AS) is the fifth leading cause of antibiotic prescriptions in children. Distinguishing bacterial AS from common viral upper respiratory infections in children is crucial to prevent unnecessary antibiotic use but is challenging with current diagnostic methods. Despite its speed and cost, untargeted RNA sequencing of clinical samples from children with suspected AS has the potential
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Re-emergence of dengue virus 3 genotype III in Cabo Verde, 2023 medRxiv. Infect. Dis. Pub Date : 2024-03-04 Menilita Dos Santos, Idrissa Dieng, Isaias Baptista Fernandes Varela, Kevin Sanders Da Rosa Carvalho, Domingos Dias Texeira, Ullardina Furtado, Liliane Hungria, Leticia Souza, Leidiza Tavares, Aliou Barry, Cheikh Tallo, Samba Niang Sagne, Ousmane Faye, Ndongo Dia, Cheikh Loucoubar, Oumar Faye, Amadou Alpha Sall, Boubacar Diallo, Moussa Moise Diagne, Maria Da Luz Lima, Abdourahmane Sow
We characterized 11 autochthonous dengue virus serotype 3 cases from Santiago and Fogo islands (Cabo Verde), 14 years after Cabo Verde's latest noticed DENV outbreak involving this serotype. Identified viruses are closely related to Asian strains and falling into a clade distinct from known circulating West African DENV-3/Genotype III isolates.
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Intrahost evolution leading to distinct lineages in the upper and lower respiratory tracts during SARS-CoV-2 prolonged infection medRxiv. Infect. Dis. Pub Date : 2024-03-04 Majdouline El Moussaoui, Sebastien Bontems, Cecile Meex, Marie-Pierre Hayette, Marie Lejeune, Samuel L Hong, Simon Dellicour, Michel Moutschen, Nadine Cambisano, Nathalie Renotte, Vincent Bours, Gilles Darcis, Maria Artesi, Keith Durkin
Accumulating evidence points to persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in immunocompromised individuals as a source of genetically divergent, novel lineages, generally characterised by increased transmissibility and immune escape. While intrahost evolutionary dynamics of the virus in chronically infected patients have been previously reported, existing knowledge
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Sex differences in symptomatology and immune profiles of Long COVID medRxiv. Infect. Dis. Pub Date : 2024-03-04 Julio Silva, Takehiro Takahashi, Jamie Wood, Peiwen Lu, Sasha Tabachnikova, Jeffrey Gehlhausen, Kerrie Greene, Bornali Bhattacharjee, Valter Silva Monteiro, Carolina Lucas, Rahul Dhodapkar, Laura Tabacof, Mario Pena-Hernandez, Kathy Kamath, Tianyang Mao, Dayna Mccarthy, Ruslan Medzhitov, David van Dijk, Harlan Krumholz, Leying Guan, David Putrino, Akiko Iwasaki
Strong sex differences in the frequencies and manifestations of Long COVID (LC) have been reported with females significantly more likely than males to present with LC after acute SARS-CoV-2 infection1-7. However, whether immunological traits underlying LC differ between sexes, and whether such differences explain the differential manifestations of LC symptomology is currently unknown. Here, we performed
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Dengue Viremia Kinetics and Effects on Platelet Count and Clinical Outcomes: An Analysis of 2340 Patients from Vietnam medRxiv. Infect. Dis. Pub Date : 2024-03-03 Nguyen Lam Vuong, Nguyen Than Ha Quyen, Nguyen Thi Hanh Tien, Kien Duong Thi Hue, Huynh Thi Le Duyen, Phung Khanh Lam, Dong Thi Hoai Tam, Tran Van Ngoc, Thomas Jaenisch, Cameron P Simmons, Sophie Yacoub, Bridget A Wills, Ronald Geskus
Background: Viremia is a critical factor in understanding the pathogenesis of dengue infection, but limited data exist on viremia kinetics. This study aimed to investigate the kinetics of viremia and its effects on subsequent platelet count, severe dengue, and plasma leakage. Methods: We pooled data from three studies conducted in Vietnam between 2000 and 2016, involving 2340 dengue patients with daily
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SARS-CoV-2 diversity and transmission on a university campus across two academic years during the pandemic medRxiv. Infect. Dis. Pub Date : 2024-03-02 Amanda M Casto, Miguel I Paredes, Julia Catherine Bennett, Kyle G Luiten, Jessica A. O'Hanlon, Peter D. Han, Luis Gamboa, Evan McDermot, Melissa Truong, Geoffrey S Gottlieb, Zack Acker, Caitlin R Wolf, Ariana Magedson, Natalie K. Lo, Devon McDonald, Tessa C Wright, Kathryn McCaffrey, Marlin D Figgins, Janet A Englund, Michael Boeckh, Christina M Lockwood, Deborah A. Nickerson, Jay Shendure, Timothy
Institutions of higher education (IHEs) have been a focus of SARS-CoV-2 transmission studies but there is limited information on how viral diversity and transmission at IHEs changed as the pandemic progressed. Here we analyze 3606 viral genomes from unique COVID-19 episodes collected at a public university in Seattle, Washington (WA) from September 2020 to September 2022. Across the study period, we
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Age-Specific All-Cause Mortality Disparities by Race and Ethnicity During the COVID-19 Pandemic medRxiv. Infect. Dis. Pub Date : 2024-03-02 Jeremy Samuel Faust, Benjamin Renton, Tasce Bongiovanni, Alexander Junxiang Chen, Karen Dorsey Sheares, Chengan Du, Utibe R. Essien, Elena Fuentes-Afflick, Trent T. Haywood, Rohan Khera, Terris King, Shu-Xia Li, Zhenqiu Lin, Yuan Lu, Andrew D.A. Marshall, Chima D. Ndumele, Ijeoma Opara, Tina Loarte-Rodriguez, Mitsuaki Sawano, Kekoa Taparra, Herman A. Taylor, Karol E. Watson, Clyde Warren Yancy, Harlan
BACKGROUND. The end of the public health emergency provides an opportunity to fully describe disparities during the Covid-19 pandemic. METHODS. In this retrospective cohort analysis of US deaths during the Covid-19 public health emergency (March 2020-April 2023), all-cause excess mortality and years of potential life lost (YPLL) were calculated by race or ethnicity overall and by age groups (ages <25
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Digital Nanofluidic Chip for Simple and Highly Quantitative Detection of HPV Target medRxiv. Infect. Dis. Pub Date : 2024-03-02 Li Liu, Stephen Dollery, Gregory Tobin, Guoyu Lu, Ke Du
Quantitative analysis of human papillomavirus (HPV)-infected cervical cancer is essential for early diagnosis and timely treatment of cervical cancer. Here, we introduce a novel energy transfer-labeled oligonucleotide probe to enhance the loop-mediated isothermal amplification (LAMP) assay for highly sensitive and specific detection of HPV 16. Conducted as a single-step assay within a digital nanofluidic
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Protocol For Human Evaluation of Artificial Intelligence Chatbots in Clinical Consultations medRxiv. Infect. Dis. Pub Date : 2024-03-02 Kwan Yeung Edwin Chiu, Tom Wai-Hin Chung
Background Generative artificial intelligence (AI) technology has the revolutionary potentials to augment clinical practice and telemedicine. The nuances of real-life patient scenarios and complex clinical environments demand a rigorous, evidence-based approach to ensure safe and effective application. Methods We present a protocol for the systematic evaluation of generative AI large language models
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Laboratory validation of a clinical metagenomic next-generation sequencing assay for respiratory virus detection and discovery medRxiv. Infect. Dis. Pub Date : 2024-02-29 Jessica Karielle Tan, Venice Servellita, Doug Stryke, Emily Kelly, Jessica Streithorst, Nanami Sumimoto, Abiodun Foresythe, Hee Jae Huh, Andrew Bliss, Jenny Nguyen, Miriam Oseguera, Noah Brazer, Jack Tang, Danielle Ingebrigsten, Becky Fung, Helen Reyes, Melissa Hillberg, Peter Mourani, Charles R Langelier, Mikael de Lorenzi-Tognon, Patrick Benoit, Charles Y Chiu
Tools for rapid identification of novel and/or emerging viruses are urgently needed for clinical diagnosis of unexplained infections and pandemic preparedness. Here we developed and clinically validated a largely automated metagenomic next-generation sequencing (mNGS) assay for agnostic detection of respiratory viral pathogens from nasopharyngeal swab, bronchoalveolar lavage and tracheal aspirate samples